Notes

Preparation

See prep (source prep.Rmd) on manipulations to go from original OTU_table_taxa_all.txt to the otu.csv used in this visualization.

You can see the Rmarkdown source for this doc at index.Rmd.

Interactivity

You can interactively filter and view data above with:

  • date slider. Drag slider to define date range to display.
  • map box: Click on box button in upper left to limit range.
  • plot legend: Click on legend labels to turn on/off sites in plot and hover mouse to get values for date.
  • table row: Click on rows to highlight selection in map and plot.

Issues

Issues:

  • map. Markers at each site are plotted for each date sampled, whereas they should be aggregated across the filters selected (requires Shiny).
  • taxa. Taxonomic filters are not feasible without aggregating also by site and/or date (requires Shiny).

Next Steps

Experimenting with time-space-taxa filtering and display using Crosstalk which enables knitting from Rmarkdown (see source) to HTML for free easy hosting on Github Pages.

Although Crosstalk synchronizes a shared data object between htmlwidgets such as the leafet map, plotly plot, and DT table, the need for aggregation across time, taxa and/or sites, necessitates migrating this type of application to Shiny for applying back-end R functions to aggregate data as interactively specified by the user.

Shiny requires a hosted solution with Shiny Server or ShinyApps.io. I’ll proceed with installing the open-source Shiny Server in the Google Cloud Platform.